rs7684418

Variant names:

• chr4-113440730-G-A
• rs7684418
• ENST00000683023.1:n.*29+14996C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000683023.1(CAMK2D):​n.*29+14996C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,160 control chromosomes in the GnomAD database, including 501 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (501 hom., cov: 31)
• Consequence: CAMK2D ENST00000683023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

CAMK2D (HGNC:1462): (calcium/calmodulin dependent protein kinase II delta) The product of this gene belongs to the serine/threonine protein kinase family and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells, the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a delta chain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Distinct isoforms of this chain have different expression patterns.[provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK2D	ENST00000683023.1	n.*29+14996C>T		intron_variant	Intron 18 of 19			ENSP00000507073.1

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11858 AN: 152042 Hom.: 501 Cov.: 31

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0857

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0804

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0780 AC: 11864 AN: 152160 Hom.: 501 Cov.: 31 AF XY: 0.0768 AC XY: 5712 AN XY: 74390

Gnomad4 AFR AF: 0.0667

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.0859

Gnomad4 SAS AF: 0.0687

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0857 Hom.: 298

Bravo AF: 0.0776

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.3
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7684418; hg19: chr4-114361886;